Acid rain in Canada and New England has caused hundreds of lakes to be devoid of fish, and in some cases, any life at all.

Impact on Forest

In New England and the southern Appalachians, millions of acres of high elevation forests have been devastated (by acid rain.

Sulfur dioxide and nitrogen oxides, the main precursors of acid rain, have been steadily decreasing in the United States due to clean air legislation and strict emission limits.

Impact on Humans and Structures

Inhaling dry sulfate and nitrate particles appears to increase the occurrence of respiratory illnesses, such as asthma. Buildings and monuments made of limestone and marble break down when exposed to acid rain. The paint on homes and automobiles is likewise degraded.

Damage is decreased because of efforts to reduce chemicals that contribute to acid rain.

Conclusions from article and graph.

Acid rain emissions are trending downward.

Using less fossil fuels and capturing or converting the pollutants might help reduce sulfur dioxide and nitrogen oxide.

Cells were not discovered until the seventeenth century, when the microscope was invented.

Three different microscopes produce images for different purposes:

Compound: for viewing by human eye.

Transmission Electron (TEM): for photographic film.

Scanning Electron (SEM): three dimensions.

Magnification, Resolution and Contrast

Magnification…The path of light rays and electrons moving through space is wavelike but the wavelength of electrons is much shorter than the wavelength of light.

Resolution… is the minimum distance between two objects that allows them to be seen as two separate objects.

Contrast… a difference in the shading of an object compared to its background.

Illumination, Viewing, and Recording

The human eye can view microscopic images when:

Light rays are bent (refracted) and brought to focus as they pass through glass lenses.

Electrons are directed toward a screen that are sensitive to their presence.

Confocal Microscopy… can create a three-dimensional image from a laser beam scanning across a specimen and producing a series of optical sections.

Video-enhanced Contrast Microscopy… a television camera converts the light image into an electronic image, which can be entered into a computer. The computer makes the darkest areas of the original image darker and the lightest areas of the original much lighter.

Two people with the same genes can be different. Scientists attribute this to nature (genes) and nurture (lifestyle & environment). A third force affecting overall welfare, a bridge between nature and nurture, is epigenetics.

Epigenetics are heritable changes in gene expression without changing the DNA sequence. Chemical reactions due to environmental exposures influence how genes are turned on or off (strengthened or weakened).

Discordant diseases in identical twins have different DNA methylation on certain genes.

Anxiety and calmness can be created by injecting or removing methyl groups with drugs. Epigenetic medicines could correct or reverse disorders.

Questions to Consder

How does epigenetics affect transcription and translation?

Methyl group attachment prevents transcription and the gene can not translate.

A parent should allow nature and apply nurture but the environment always holds a trump card – and its blowin’ in the wind. Class mates and food takes can grab your tikes by the genes and never let go. It’s no wonder non-twins from the same parents with the more or less same nature and nurture grow up to become so different when you consider all of the environmental factors which are out of the parents control and growing, literally, out of control.

Traditionally, a scientist would isolate one species to culture enough DNA for sequencing resulting in the loss of the true biodiversity that existed in the sample.

Shotgun Sequencing (SS)

SS randomly shears DNA, sequences the short fragments, then reassembles these sequences into the correct order – called consensus sequence.

Eukaryotic DNA can be identified and removed, leaving the microbial DNA behind for analysis.

Studies Using Metagenomics

…does each type of mammal have its own community of (gut) microbes?

…the diet of mammals, not the specfic species of that mammal, determines what microorgansms live in the gut.

Metagenomics can also be used as a diagnostic tool to discover causative agents of diseases.

Questions to Consider

Why is metagnomics used versus traditional genomic techniques?

Traditional science isolated and cultured only the most abundant species, resulting in the loss of the true biodiversity that actually existed in the collected sample, metagenomics allows for determining evolutionary interactions in a particular environment by revealing the hidden biodiversity of microscopic life.

2. Why is shotgun sequencing used in the field of study?

In order to gain knowledge on the true biodiversity of all species in a given environmental sample:

SS takes pieces of DNA and sequences the short fragments into the correct order.

The result is defined as a consensus sequence.

3. Why is metagenomics closely tied to evolutionary biology?

When used as a diagnostic tool, it can be used to discover causative agents of disease, such viral evolution, by filtering out DNA of a healthy species to reveal the disease in a sick subject.

Comment:

I don’t get the explanation of Shotgun Sequencing provided by the author. SS got its name from the broad trajectory of buckshot a shotgun blast produces. Then, SS is likened to putting ten copies of the textbook in a shredder, taking those pieces out and reassembling a complete book.

Without going further, two consecutive metaphors (1 metaphor, 1 simile) leaves a cub-metagenomicist with a rapidly spinning propeller. I think I would try to reconcile the two metaphors before giving an explanation that doesn’t seem to address either. There must be a better definition of Shotgun Sequencing out there.